This folder contains code for the analysis of the CK/CK-p25 mouse data. Some code overlaps with analysis code in Welch et al, Sci. Adv. 2022
load_counts.R (loads the expression data)
load_metadata.R (loads the metadata)

preprocess/ contains scripts for aligning, running STAR-fusion (03_star_fusion.sh), calling cell types, and aggregating outputs.
analysis/ contains scripts for analysis of the expression and fusions data, most relevant are:
plot_00_umaps.R and plot_00b_genes.R (plotting genes and metadata on the UMAP)
plot_04b_split_trajectory.R (creating trajectory from Welch et al. that is used in Figure 1)
plot_07_fusions.R (preliminary fusions analysis)
plot_07_fusions_signif.R (final fusions analysis)
plot_07a_fusions_umap.R (plot of fusions on the UMAP basis)
plot_07b_fusions_stratify.R (fusions against gene signatures)

Loading functions for data in R:
load_basic_fusions.R (fusions data)
load_go_signatures.R (gene set signatures)
load_umap_basis.R (umap, cell metadata)